How to Generate tissue_lowres_image.png from tissue_hires_image.png for spatial transcriptomics?
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Entering edit mode
4 months ago
Genomancer • 0

Hi everyone,

I’m working with spatial transcriptomics data in Seurat but only have these files:

filtered_feature_bc_matrix.h5 
tissue_hires_image.png
tissue_positions_list.csv
scalefactors_json.json

I need to generate tissue_lowres_image.png because my system can’t handle the high-res image because I'm working with multiple tissues, is there a tutorial on how to downscale tissue_hires_image.png or how to create the tissue_hires_image.png?

Either Python or R will be fine

seurat spatial-transcriptomics • 614 views
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Entering edit mode
4 months ago
GenoMax 151k

Is this 10x spatial data? File names seem to indicate so. While someone provides an answer this is what 10x support says about the tissue images.

https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/spatial-outputs

my system can’t handle the high-res image because I'm working with multiple tissues

As in you don't have enough memory?

It looks like Seurat can handle high-res images based on this comment --> https://github.com/satijalab/seurat/issues/5614#issuecomment-2105263800 but that is likely not the question you are asking.

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Entering edit mode

sorry for the incomplete question. Yes, its 10x spatial data and I'm having trouble comparing the multiple tissues because I don't have enough memory I used the calculations in the 10x support in the link you provided and I was able to solve the problem. thanks

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